Back in the rotation with Frederick in 2003, he was 4-9 with a 3.34 ERA. Returning to relief in 2004, he bombed, going 1-7 with a 5.61 ERA; he walked 41 in 86 2/3 IP while striking out 52, a far from two years prior. In his third full year for the Keys, 2006, Lewis was 5-3 with six saves and a 2.09 ERA, walking 11 in 51 2/3 IP to reestablish himself.

Lewis moved up to the Bowie Baysox in 2007 and went 5-5 with a save and a 5.35 ERA, allowing a .294 average. The big southpaw went 1-6 with a 3.41 ERA for the 2008 Baysox. Opponents hit .308 and he walked 26 in 66 innings though he did fan 63, his best K rate in a few years.

Lewis began 2010 with the 51s with mixed results (0-1, 5 R, 2 ER, 10 H, 7 K in 7 2/3 IP, 5 Sv). He was then called up alongside Josh Roenicke to replace Jeremy Accardo and Merkin Valdez on the Blue Jays staff. He made his major league debut on April 28th relieving Roenicke in the 9th with a 2-0 deficit against the Boston Red Sox. He got J.D. Drew and Jason Varitek on grounders. Adrian Beltre singled then pinch-hitter Mike Lowell whiffed to end a good first inning in the Show. He did not stay as sharp the rest of the year, either in the majors (20 H, 8 BB, 14 R, 15 K in 18 2/3 IP) or the minors (1-5, 5 Sv, 7.59, 72 H, 51 R in 53 1/3 IP).

2011 was another poor performance both for Toronto (12 H, 8 R in 5 IP) and the 51s (3-3, 4 Sv, 6.60 in 42 G). Moving to the independent leagues in 2012, Lewis feasted on the weaker competition, going 3-1 with 7 saves and a 2.01 ERA for the Bridgeport Bluefish. He was named as the Atlantic League's All-Star reliever. He moved to the York Revolution for 2013 and was even better (0-1, 5 Sv, 1.51 in 47 G), earning him a contract with Taiwan's Lamigo Monkeys.